File get very confuesed by time signature changes

I'm trying to use MuseScore to figure out and transcribe a hymn that has a somewhat Celtic feel to it. It is written nominally in 6/4 time, but has many sections in 4/4 time.
If you'd like to get a sense of how it sounds, go to the artist's website here:
http://www.robinmark.com/index.php?section=9
and click on the sample for the song called "He Shall Reign."

I'm aware of some concern raised already about how MuseScore handles t/s changes (e.g. see
http://musescore.org/en/node/1499 or
http://musescore.org/en/node/1585 .)

I am still trying to learn this song, and there are many different approaches one can make to capture the t/s changes
One can choose to write three bars of 4/4, or two bars of 6/4, or change on each bar (4/4, 2/4, 4/4, 2/4). In trying to capture the essence of the song and get it all in, I made numerous edits, and copy/pastes, recognizing that changing from 6/4 to 4/4 might truncate the last two beats, or that changing a string of 4/4 bars to 6/4 introduces unwanted rests. I handled all that (I thought). Unfortunately, however, MuseScore has gotten quite confused and it is clear that my file now is irreparably corrupted. See attached.

There are barlines where there is no bar; sufficient in number to make one think that there might be about 12 bars, though the notation at the beginning of the second line (11) suggests that the s/w only identifies 10 bars in the first line.. MuseScore has placed three accidentals before the key signature (bar 15), despite the fact that there is no key change anywhere in the song; it's all written in AMajor. If you use playback on the attached file you'll notice some very odd behaviour, especially between bars 22 through about 27. At bar 33, the playback actually goes backwards at one point.

I am forced to restart with a clean file and try to re-input from scratch I think. My recommendation is that for songs that have lots of time signature changes, users only use MuseScore to capture the song in a linear method, not to use it as a "scratchpad" to learn or try different representations like I did.